Fallout: The End
by Minecwt
Summary: The Institute has begun their attempt to destroy their enemies in the Commonwealth, starting with the Commonwealth Minutemen and Brotherhood of Steel. The final battle for the future of the Commonwealth has begun.
1. The Beginning of the End

Fallout: The End

**AN: I do not own Fallout 4 or the characters mentioned in this story.**

Arthur Maxson was angry, angrier than he usually was as the Institute and their abominations, the synth, had just attacked the Boston Airport and the Brotherhood had just barely fought them off. Along with this attack it appeared that the Institute was attacking his forces across the Commonwealth.

Maxson's attention was brought back to the report he was getting from Lancer Captain Kells. "We also lost contact with several of our research and vanguard patrols shortly before Institute attack. And Cambridge Police Station has not reported in for several hours." That got Maxson's attention. If the Institute had managed to occupy Cambridge then they had effectively forced the Brotherhood out of the heart of the Commonwealth and away from the ruins of the Commonwealth Institute of Technology, which the Institute was supposedly built under. "Sir?" Kells asked, waiting for orders.

Maxson shot his head back towards Kells and realized that he had not given Kells any orders or ways to prepare for their counter attack. "Get together a fireteam and give them a vertibird and have them reestablish contact with the police station." Kells snapped to a salute and then ran off.

The absence of the Lancer Captain gave Maxson time to look around the Airport. The main force that usually occupied the area around the walls were gone, either dead, injured or patrolling the vicinity around the airport. The walls however were manned by some of the Brotherhood Light Knights. Liberty Prime was patrolling just to the east of the Airport. They were lucky that the Brotherhood had managed to activate Liberty Prime before the Institute had been able to do whatever they were trying to do with it. Several of his soldiers had been placed back in the terminal, where Knight Captain Cade was working to save their lives.

Maxson made his way over to them and looked over the soldiers, these were the badly hurt ones. The ones who had been only lightly injured were still on patrol or manning the walls. Maxson knelt down next to one soldier quickly identifying her as a Knight Rebecca Miller. "Knight Miller, how are you feeling?"

The Knight seemed surprised that the Elder of the Brotherhood was talking to her, and it took her a moment to respond "Fine Sir, Knight Captain Cade says that I should be back on my feet in a couple of days."

Maxson smiled and said "Good" Maxson was going to continue to the conversation, but several scribes moved into the room to help Cade. So, he decided it would better to just get out of their way.

Maxson decided it was now time to get back up the Prydwen and begin to plan for the Brotherhood's counterattack against the Institute. If they were able to, he wanted to launch it at the earliest possible time, hopefully tomorrow, but that depended on whether or not he could count on the forces at Cambridge. If they had been wiped out, he might have to send back to the Capital Wasteland for reinforcements, which Arthur really did not want to, as then that would compromise their operations against the remains of the super mutant army there and Arthur didn't want to give them a chance to organize themselves. But on the chance that the forces in Cambridge Police Station had been able to survive what ever the Institute had thrown at them, then they could then they could launch an attack. These problems weighed on his mind during the flight back up to the Prydwen, and then has he entered the command deck.

Maxson had had a map laid out before the attack on the Airport had begun and he had placed markers on Brotherhood locations across the Commonwealth, along with placing other forces within the wasteland, the Minutemen at their Castle to the south, they were led by the former Brotherhood Knight John Pershing. To the west was the largest settlement withing the Commonwealth, Diamond City led by its mayor, a man by the name of McDonough. Diamond City had refused both Minuteman and Brotherhood request to place a garrison in the city preferring to go at it alone with their own small defense force. Also to the west and a bit closer to the Airport was the settlement of Goodneighbor. Of all of the settlements in the Commonwealth the Brotherhood had very little to do with Goodneighbor, instead at Maxson's directive, the Brotherhood had given it a wide berth as so neither his soldiers or the people of Goodniegbor could cause an incident.

There was loud bang as the door to the command deck was closed carelessly and the familiar clang of powered armor running on the metal. Maxson looked up at the Knight who was now before, about to issue a reprimand on how to be careful with the Brotherhood's equipment but the Knight began speaking before he could. "Elder, the Minutemen's Castle is under attack from the Institute."

That was certainly a surprise that Maxson had not been expecting "How do you know this Knight?" he demanded.

"I was on a vertibird returning to the Prydwen and we flew over the Castle. With our communications down, we thought it best to come back and inform you sir."

"You did well to inform me, go and report in to your commanding officer" The Knight attempted to salute in the armor and then left. The information he had been given changed things. It appeared that the Institute was now attempting to launch an attack on all of their potential enemies, not just their overt ones. Maxson looked down back at the map and knew he had to decide whether or not the Brotherhood was going to come to the Minutemen's aid. As he looked at the map he realized that there really wasn't any decision to made.


	2. The Defense of the Castle

**A/N: I do not own Fallout 4 or any of the characters in it.**

Preston Garvey knelt down to tend to one of the many wounded Minuteman soldiers that littered the ground of the Castle courtyard. This particular Minuteman had major burns on his both of his shoulders, but his leather armor had been destroyed in the previous battles. Preston bandaged the wounds to try to keep an infection out from starting. "Thank you, sir." The Minuteman said has he struggled to move to look up at him.

Preston simply nodded and got up and took in the sight, Minuteman troops patrolled the walls while their medic forces attempted to save the many Minuteman that had been injured. Looking at the sight made Preston realize how much he truly hated the Institute. The Minuteman had never bothered them, they were just trying to help the people of the Commonwealth, but the Institute had attacked them. Even now nearly an hour after the battle had concluded Minuteman artillery kept the Synths that were still attempting to breach the walls contained. A set of heavy footsteps made Preston look up.

"Preston, I want you to take your squad and get back on the northern wall, the bastards are preparing for another attack." General John Pershing, the Sole Survivor of Vault 111, started. "We don't have the artillery shells to keep the barrage and when we quit the Institute's going to hut us with everything they have here."

Preston nodded and asked "Has Lewis been able to get back into contact with the any of our settlements?"

Pershing nodded his head and said "No, but we have to keep our thoughts here. If were defeated here then the rest of the settlements won't have a hope of defeating these bastards."

Preston had to agree with that. The different settlements alone didn't have the manpower or the will to fight against the Institute without the protection that the Minuteman provided. But Preston had to put thoughts like that out of his head, they had a battle here and now that needed winning. He looked over to his squad who were sitting against the stairs that lead up to the defensive positions.

One of the soldiers who were standing up looked at him and asked "What's the plan Colonel?" 

"Were moving to support our men on the northern wall, the Institute going to hit us soon and we need to be prepared for anything."

A few moments later, Preston and the squad were on the wall and looking towards the city ruins. The artillery bombardment continued but was beginning to slow down. Preston knew that the coming hours would either see the Minuteman emerge victorious, or they would fall apart for the second time in a single year. Preston faintly heard The General give the order for the artillery to stop firing. Preston swallowed and the firing stopped and then all hell broke loose.

The Synths launched themselves from their positions in the city, as the Institute also relayed in synths closer to the Castle walls. "Open Fire!" Preston yelled and fire, both ballistic and laser erupted from the walls of the castle. Several of the synths fell as the fire overwhelmed them, but the synths kept coming. Preston cranked two more rounds into his Laser Musket and fired into the crowd. The fighting continued like this for several more moments, before in another flash blue appeared, but this time much closer. The Institute had relayed synths onto the walls of the Castle itself. Preston turned and fired into one of the synths who had just rematerialized. The Minuteman who had been focused on the battle going on outside the walls shifted their fire to the fight that was now taking place across the courtyard and the top of the walls. Preston took a moment to survey the battle taking place in the rest of the Castle. The Institute had overrun the western wall, and the Minutemen who had been defending the wall had been forced onto the courtyard and were slowly being picked off by the Synths. Luckily the eastern walls had not fallen to the Institute, and the Minutemen stationed there had begun attacking the synths. Preston smiled, for a second there he had thought they had had lost the battle, but there was still hope.

General John Pershing was not feeling hopeful about the situation at hand. The Institute was pushing hard on the western walls, and Preston and his men were still in a fight for their lives on the northern wall. Ronnie Shaw was leading the charge from the eastern walls, and Danse was with him. Despite the setbacks, he was not willingly to let the Institute to have the Commonwealth however. John looked back to the battle at hand, the Institute had taken the northern wall, and he and Danse were trying to plug the hole in their defenses. He had just taken a shot with his R91 Assault Rifle when he heard it. Rotor blades which belonged to Vertibirdd, and there was only one faction that had access to that kind of pre war tech. John looked up and saw five Vertibirds dropping down towards the Castle, one of the vertibirds swung around to reveal its minigun as it opened up on the western wall, Powered Armored soldiers dropped from the other across the entire battlefield. It was then that John remembered that Danse was a synth and what the Brotherhood thought about synths.

"Danse!" Danse looked over as John continued "Here out this gas mask on!" the gas mask was one of the things that John always had on him, and today he was happy that he had it. Danse nodded his head in understanding and put it on quickly.

The General looked back at the battle, the Brotherhood had appeared to swing things back in the Minutemen's favor. And he smiled despite himself, the Institute was going to pay for what they had done to the Commonwealth, and for what they had done to him personally.

The fight was still not over yet. And John knew that. He ordered for the men that had been forced down the western walls to follow him as he charged up the stairs, straight into the Institute synths. John fired blindly into anything that resembled a synth. The fighting was intense and bloody, but the Minuteman charge succeeded and threw the Institute off of the walls. After which the Brotherhood vertibirds fired on the synths that were retreating. The Battle of the Castle was over, and the Minuteman had just won a surprise victory against the Commonwealth's boogeyman. And now John had to find the leader of Brotherhood force and figure out what they were going to do next.


	3. Planning

**A/N: I don't own Fallout 4 or any of the characters involved in this story**

"Our turret grid took a beating in the battle; the engineers think it will take another twelve hours to get it back up." Colonel Ronnie Shaw finished her report and General John Pershing was not happy.

"I will task some of my scribes to aid your engineers in your repair efforts." Elder Arthur Maxson spoke up from his seat to the right of John. An alarmed look came from Colonel Shaw but John simply waved it away.

"Thank you for the offer, and we gladly accept." John started and then looked around, the men and women that had been gathered in Pershing's office were all tired and battered from the battle, and it was likely that that was not going to change anytime soon. He looked over to Colonel Shaw's left, where the former Paladin Danse stood, hands at his back and with a gas mask on. "Soldier, have the artillerymen given you the estimates to how many shells we have left?"

Danse nodded and appeared to look over to Maxson before starting "The artillerymen report that they fired about 70% of the stock during the battle." He paused as all eyes turned to Maxson, while he appeared to have clenched his jaw, he did not say anything. "They are afraid that they won't be able hold off another attack or help any settlements if the need arises." Danse concluded his report.

Pershing sat back on his chair and rubbed his beard "Speaking of other settlements, we need to figure out if this is an isolated event or the beginning of a major offensive" and while looking back at Maxson "and considering their attack on the airport, I'm willing to bet that it's the latter and not the former."

Maxson nodded his head and said "I'm still waiting to hear back from the Cambridge Police Station." he eyed Danse and then said "If they are still operational, I am going to launch an attack on the Institute and crush them before they can attack us anywhere else."

General Pershing looked over at him and said "We should combine our forces; both the Minuteman and the Brotherhood has a dog in this fight now." He looked around and then back at Maxson "besides both our armies have taken heavy casualties in the last twelve hours, in order to help ensure our success it would be better to hit the Institute with both of our armies combined.."

Maxson looked at Pershing and nodded his head. Pershing smiled and opened a drawer on his desk and produced a map of the Commonwealth, which he laid out on the desk. Before beginning however, he looked up at Danse and Preston and said "Go and check with Major Lewis about getting into contact with the rest of the settlements. And Colonel Shaw go and get our forces ready to move out. The Elder and I will discuss strategy" The leaders of the Minuteman saluted and left the room. Leaving to two leaders alone.

Danse and the other leaders of the Minuteman left the General's office going about their assigned tasks. While walking through the inner walls Garvey said "I'm not sure how I feel about the Brotherhood being here at the Castle."

"I understand your concern," Danse stated, and while he himself was not sure on his feelings for the Brotherhood, he still believed in the ideas of why they were here in the Commonwealth. "But the Brotherhood isn't here to take over, they simply want to stabilize the Commonwealth, similar to what we did in the Capital Wasteland."

Garvey looked at him with a questioning face "How can you still believe in that good intentions of the Brotherhood after what they did to you?" They came outside of the Castle Walls into the courtyard. The injured soldiers had been moved to the area around the armory had both Minuteman medics and Brotherhood scribes tended to the wounded.

Danse shrugged and then readjusted the gas mask he was forced to wear now that the Brotherhood was here. "The Brotherhood has wronged me Garvey, but they also have helped a lot of people back in the Capital Wasteland, and they are helping to fight abominations here in the Commonwealth."

Garvey sighed, signaling an end to the conversation, as the finally reached the communications center which in truth was simply a radio tower in the middle of the Castle courtyard with a ham radio hooked to it, and Major Jacksons Lewis sat at the center of it. He was in deep conversation with the other end of it. "Understood, I'll get the General informed right away."

Lewis looked up at Preston and Danse who had taken to standing near the man. "That was Sanctuary" he said quietly "It looks like the Institute hit the northern settlements pretty hard as well." He looked down at the notes he had taken during the radio call. "Sanctuary reports that they were able to fight off the synths, and that Sturges had the garrison go aid the forces at Starlight."

"Hell" Preston said, his tone and face concerned. "Starlight, Sanctuary and Sunlight are our largest settlements, if they were trying to take the north then the Institute was truly trying to destroy us." The Major shook his head in agreement.

Danse then asked "What about the other settlements? Have you been able to re-establish communications with them?"

Lewis nodded his head and said "The settlements that have radios have radioed in and let us know that they haven't seen any sign of the Institute, and I doubt that the Institute would bother with the smaller settlements, most of those are simple farming villages."

Danse nodded his head just as he heard the unmistakable sound of Vertibird rotor blades overhead, and looking up he saw another Brotherhood Vertibird landing just outside the main entrance to the Castle. Both Danse and Preston ran towards the entrance to greet the new arrivals, and Danse realized that he had made a mistake coming as the Brotherhood soldiers might find out who he was. Jumping out of the Vertibird as they arrived was a three-man squad in Power Armor. The lead man was in the standard issue T-60 Power Armor, with a Knight-Captains insignia on his right arm. "I was informed that Elder Maxson is here, I have information that I am supposed to give him right away, take him to me" he ordered more than asked.

Danse spared a look at Garvey and realized that it would not be best if he answered, and then Danse said "Very well follow me." The Knight-Captain regarded Danse for a moment and then motioned for him to lead on.

General Pershing and Maxson stood on his side of the desk as the Brotherhood soldier gave them their report. "Cambridge has not fallen to the enemy, but the Institute did attack them there sir."

Maxson rubbed his beard and said "Good they will be instrumental in our counter attack against the Institute." He looked back at the General and then ordered "Now get your squad patrolling the outskirts this fortification. And kill any of those abominations that you come across." The soldier nodded the best he could in the Power Armor and then left the office, leaving Maxson, Pershing, Danse and Garvey alone.

"Ok Garvey" Pershing started "has Lewis been able to get back into contact with our settlements? 

"Yes Sir, he reports that the northern settlements have been hit hard, and before we came back in, Starlight reported that both it and Sanctuary have been able to fight off the attacks, but there hasn't been any word from Sunshine."

Pershing rubbed his eyes and took a second to think. It was good that they hadn't lost more to this offensive, but if the Institute was able to establish a base at Sunshine then the northern settlements would be at risk, and they would have they hands on the artillery also at Sunshine.

"Isn't Sunshine where one of your artillery emplacements is?" Maxson asked, but based on his face, it appeared he already knew the answer.

Pershing answered anyway "Yes, let us hope that the Institute hasn't taken it."

"Sir" Preston said, there is one other thing I think you would be interested in." Pershing looked up and motioned for him to continue. "Sturges also got on the radio and sent over schematics to a back way into the Institute through some of the sewer tunnels from the looks of it." Pershing smiled and now he knew what to do.

Looking over at Maxson Pershing answered "Good, we can hit the Institute from the place they're least expecting."

"My Brotherhood could still attack from the top provide a overt attack to supplement your sneak attack, and then once we both get there we can meet up in the Institute proper and destroy the beast."

"I agree" Pershing said "I think that is the best plan" he stood up as he continued "You should return to the Prydwen and prepare your forces while I prepare mine."

Maxson nodded his head and said "I agree, once I feel prepared, I'll radio my go ahead and send a vertibird to pick up your forces from here and land you closer to the area." Maxson then held out his hand and Pershing took it.

"Radio us when you're ready and we will ensure that the Institute won't have to power to do this ever again."


	4. Chapter 4

**A/N: I don't Fallout or any of the characters in this story. Also I wanted to apologize to the readers that I have not posted in a while, that was something that I did not intend to let happen. **

Piper Wright picked up her pace as she neared the Minuteman's Castle. She had started her way there when she heard the massive artillery bombardment. While artillery being used had become relatively normal to hear, the shear amount of artillery that was fired worried her that the Castle had come under attack. She had felt compelled to go as soon as she heard the artillery bombardment. for two reasons, to make sure that the Minuteman had or at least were going to win the battle, and to make sure that John was okay. Her pace quickened again when he came to her thoughts, and a pang of concern came with it. 'It's okay Piper' she told herself 'John fought in the war, if half of the stories you've heard from him are true then he should be fine.' She finally came out of the city and got a good look at the Castle.

The Castle has seen better days, smoke came from the walls and the turrets lining them and the building that sat around the Castle itself had been leveled. Craters also filled the land around it. Institute Synth and Minuteman remains littered the battle ground, and to her surprise so did Brotherhood soldiers lay dead. Despite the damage to the Castle, it was still standing and under the control of the Minutemen. As she got closer to the walls Piper could make out scorch marks from the battle.

"STOP AND IDENTIFY YOUR SELF!" she stopped immediately and turned her head to look at the Minuteman, one she did not recognize, who yelled.

"I am" She was cut off by another Minuteman, this one she recognized and recalled that his name was Met.

"That's that the reporter from Diamond City, the one that's always hanging around the General" Met stated, looked at her and said "Let her inside, the General's in a meeting" Hearing

She nodded at him and said thanks, and went through the entry way. And came upon a sight that she had not been prepared for. Many Minuteman had been laid in a make shift hospital in the far corner of the Castle interior, doctors went through trying to help them. Another corner looked to have been where they placed the Minuteman who did not survive the battle. A thought came to Piper's head and she grabbed her note book to write it down. _In the next issue of the Publik, put the names of the fallen at the end to make sure that they are remembered. _While she knew that odds of being able to actually identify some of the bodies would be an arduous task, it would be worth it.

Piper wondered how many Minuteman had fallen in the battle, and if this was larger than just the Castle, how many people had died in the past day? She shuddered at the thought, and figured that she didn't want to know anyway. Piper knew she should probably go and see John, make sure how he was holding up after all of this. She began to walk to his office on the inside of the walls.

Piper went in around a makeshift surgery area. She heard one of the medics yelling "Were going to need to cut his leg off if he's going to live." That worried her, how would a one-legged man make it out there in the wasteland? After all this was over, she would have to ask John how he was going to deal with that.

She finally came to the door that led into John's office/bedroom, she gingerly knocked on the door and heard a gruff and tired sounding "Come in."

She opened up the door and slipped in and closed in. John sat there studying a map, with a cigar in his right hand. He looked up at her and looked surprised asking "Piper? When did you get here?"

She smiled and said "I just got here ten minutes ago. The guards said you were in a meeting." John sighed and took a drag from the cigar.

She got serious and asked "What are you going to do John?" she asked, his face didn't give anything away and then added on "The Institute attacking one the key organizations in the Commonwealth isn't good.

Taking another drag from the cigar he answered "No its not, and its even worse than you think." That confirmed her fears that this wasn't an isolated attack. "The Institute attacked the northern settlements and the Brotherhood at the airport and Cambridge." The mention of the Brotherhood put a bade taste in Piper's mouth.

"That explains the Brotherhood soldiers I saw galivanting outside." John looked at her disapprovingly.

"The Brotherhood came here and gave us support as the Institute launched its final assault, I'm not sure we could have held on without them." He took final drag of cigar and put it out. "And besides, the Brotherhood is now an ally in this fight, and we need all of the allies we can get to win this thing."

Piper nearly laughed at him. The Brotherhood didn't just do things to help the community, there was always an underlying motive with them. "And what do you think that the Maxson's going to want out of you for this?" she demanded.

John rolled held up his hands and said "The Brotherhood hates the Institute as much as the rest of the Commonwealth." That wasn't the answer Piper wanted and she opened her mouth to tell him that, but she was cut off. "Look Piper, we need the Brotherhood, and the Brotherhood needs our help to stop the Institute, we both took heavy casualties in the Institute's offensive."

While that did kind of satisfy her, she still thought they wrong and muttered under her breath, "You're trading in one devil for a slightly less evil devil."

John either didn't hear it or just didn't respond, which Piper took as a victory. He stood from the desk and said "Piper for the time being, I want everything I have just told you to be off the record okay?" he ordered in a way that made it seem like she had a choice in the matter. Realizing what he did he added on, "After all of this is over, we can sit down and have a proper interview about what's happened.

Piper smiled and said "I would like that very much."

John looked about ready to say something else when a Preston Garvey and Danse came barging into the office. "General" Preston started "Maxson just radioed that he is ready to commence with the attack."

She looked over at John who asked "Are we ready?"

Danse answered "Yes sir." John nodded and had them leave to get the Minutemen ready.

"Good bye, Piper, I'll see you again after all of this." and went to leave the room.

As he did, she said "Come back, I want that interview."

Piper followed them outside a few seconds later to see a singe Vertibird take off with John, Preston, and Danse." Come what may, she knew that the Commonwealth would never be the same after today.


	5. Chapter 5

**A/N: I don't own Fallout 4 or any of the characters in the game. **

Elder Arthur Maxson's Vertibird followed behind Liberty Prime, as the giant robot made its way across the Commonwealth towards its goal of the Institute. Brotherhood soldiers followed close behind and in front of the robot. Maxson had mobilized the majority of his forces in the Commonwealth for this attack, even now as his forces crossed the Commonwealth, the forces at Cambridge police station under Paladin Dillon were securing the courtyard of the CIT ruins. Maxson just hoped the Pershing and his force's infiltration of the Institute was on schedule if it wasn't, then the entire operation might be a failure.

"Synth forces relaying in to the front and to the west!" The Lancer yelled from the cockpit. Maxson shifted his attention to those areas and saw the blue hue that he had become are to familiar with in the previous few days.

"Bring us around!" Maxson roared, and the Vertibird moved so that the machine gun was pointed to the Synth abominations, Maxson opened fire. Three fell in the first few seconds of the barrage, but the Institute just kept on relaying more and more in. The synths kept falling. Maxson was starting to feel good about the attack, just as he heard

"SYNTHS RELAYING BEHIND US!" A Knight said as he began to open fire with his laser rife. a few moments later he yelled "ROCKETS!" 

The first rocket missed the Vertibird, but the second did not. Knowing that the Vertibird was going to go down, Maxson sprung into action, yelling for the powered armored soldiers to grab their less armored brethren. He reached out and grabbed the light knight to his left, and braced himself for the crash.

Pershing, Danse, and Preston Garvey continued to walk through the sewers. They had been in the sewer that had the secret entrance to the Institute for nearly an hour and a half, and had come across only a squad of Synths, and a few of the laser turrets. Which probably meant that they were in the right place.

"I wonder if the Brotherhood has launched their assault?" Garvey wondered out loud; Pershing spared a moment to look back his second in command. Garvey was obviously tired, with heavy bags underneath is eyes.

"They probably launched the assault as soon as we got into the sewer system" Danse answered from behind Garvey. "At least that's what would have been the most sensible thing to do."

Garvey scoffed and said "Because the Brotherhood always does the most sensible thing." Pershing sighed, knowing that both of his top officers had strong feelings about the Brotherhood, they would argue back and forth about them for the rest of the mission if he allowed it.

"Cut the chatter about the Brotherhood" turning to Garvey he said "Like it or not, the Brotherhood is now our ally in this fight. "He turned to Danse and said "We can't have this sort of infighting right now." Both men looked down and didn't say anything. "We have to keep our eye on the ball and defeat the Institute, after that we can decide what sort of relationship we need to establish with the Brotherhood." Of course, if he had it his way, the Minutemen and the Brotherhood would coexist and work together to bring peace and stability to the Commonwealth, but whether or not Maxson wanted that, or his own ranks in the Minutemen wanted that was another problem.

The sewers led to a dead end with both turns leading to the dead ends. "Spread out and try to find a way through the walls." The wall had some small holes in it, and he could see that there were rooms on the other side of the wall. "If we don't find a way, we will just blow our way through it.

They did find a small hole in the wall that they could barely fit through, and they found themselves in what looked like an abandoned workshop. "Might've been an old maintenance tunnel" Pershing decided, he looked around and spotted another door. "Looks like our way through." He motioned with his Assault Rifle and the three of them moved through it.

"Motion detected" a synthetic voice rang through the room, just before blue laser beams started to fly towards the Minutemen. Pershing barely dodged one of them as he dove for cover behind and old generator.

He turned the corner and sent a stream of bullets towards the direction of the synths. They had to take these bastards down before they were able to get word back to the Institute. He looked over at Garvey, who had taken dropped to the floor and was returning fire in a prone position. "Garvey throw a grenade!" Pershing yelled. Garvey stopped firing and reached for his grenades as Pershing tried to suppress the synths. He saw the grenade fly towards the enemy and land right and the feet of the three synths. The explosion destroyed them moments later.

Slowly, Pershing got out of cover and checked for more synths. Not seeing any he yelled "Okay, looks like were clear." He spotted a man-sized pipe and checked the schematics on his PIP- Boy that Sturges had found. "Looks like this is it." He and the others walked over to it opened the sliding door. Looking to the right just led to a dead end, so they moved to the left and followed the pipe, hoping that it would not take long to get to the Institute.

As they moved through the pipe, a was rumbling that seemed to come from above. The sewage water they sat in splashed as it reacted to it, and dust fell from the ceiling, looking up Garvey stated "Sounds like the Brotherhood is getting closer, had to of been a mini-nuke to cause that sort of thing"

"Or one of Liberty Primes nukes" Danse stated "When we -"he stopped abruptly, and then started back "When the Brotherhood used Liberty Prime back in the Capital Wasteland, if you were close to the battle, you had trouble staying on your feet."

"Wish we had that thing back in Alaska" Pershing muttered under his breath. "Would've saved a lot of lives. Of course, it probably wouldn't have mattered much anyway." He finished his thought bitterly. Behind him both Danse and Garvey looked at each other. It wasn't often that Pershing talked about his life before the wasteland. He looked behind himself and said "Let's keep going c'mon."

Arthur Maxson coughed and looked around his surroundings, the Vertibird had gone down hard, and many of the lighter armored soldiers were badly hurt or dead. The Knights and Paladins that had been following behind Liberty Prime had fallen back and formed a perimeter around the fallen Vertibird. And were currently fighting the synths around the Vertibird and keeping the synths from attacking the survivors.

A field-scribe ran up to the Vertibird and pulled the Knight off of Maxson. "Elder," another scribe yelled. "Are you okay?"

"I'm fine, check on the others." Maxson yelled. The scribe nodded and went off to aid the wounded. Maxson pulled himself out of the destroyed Vertibird, and grabbed his Laser Rifle. He ran toward the front of the perimeter, where the fighting was the thickest. The Paladin in charge of the perimter looked at him. "What's the situation Paladin?" he asked.

"The Synths are pushing us across the perimeter!" The voice of Paladin Brandis answered him" He pointed to the direction of the CIT ruins. "The rest of the force, along with Liberty Prime, have continued on towards CIT!" As he was reporting this, his hand was hit with the blue laser of a Institute Laser Rifle. Maxson turned shot the perpetrating Synth.

"As soon as the casualties are loaded back onto the gunships, we need to move!" Maxson yelled over the fighting. The fighting was fierce defending the perimeter, and Maxson was suddenly wishing that the Brotherhood had been able to bring their own artillery to the Commonwealth, but that was unfeasible with deconstructed Liberty Prime having been brought as well. As the last of the Vertibirds took off and flew back off to the Prydwen.

"MOVE OUT!" Maxson roared and the Brotherhood soldiers began too. Maxson led the force as they finished the last leg of the journey to the CIT ruins. The area leading to CIT had seen heavy fighting and craters from Liberty Prime's nukes littered the way. To Maxson's relief, it appeared as though the Brotherhood had taken minimal casualties to the Institute. Just as CIT entered his view, he could see the fighting there was intense. "DOUBLE TIME IT!" He yelled as he broke out into a sprint, as did the rest of the soldiers following him.

As they reached CIT, Liberty Prime destroyed the left side of the building with one of his nukes. Scribe Ingram ran over to him and yelled. "Good to see you sir." She looked up to Prime and said "He needs time to locate where the Institute is under there!"

Elder Maxson nodded and yelled "DO WHAT EVER YOU HAVE TO TO PROCTECT PRIME SOLDIERS!" as he finished giving the order, more Institute synths relayed in. Maxson took aim at the first one and fired, killing it instantly, as did the soldiers around him. Maxson vaguely heard Prime say that he had found where the Institute was and saw him as the robot fired a drilling beam into the ground. "KEEP FIGHTING PRIME'S ALMOST DONE!" The synths were slowly destroyed, and the reinforcement stopped relaying in. 'They must be pulling back to prepare for our attack in the Institute itself.' He thought as he and his soldiers ran to the hole that Liberty Prime had just stopped drilling. "Let's go! For the Brotherhood!" Maxson yelled the war cry as he jumped into the hole.


	6. The Nuclear Option

General Pershing watched as Sturges and Proctor Ingram slowly got the teleporter working. To his left, Elder Maxson paced impatiently, Maxson, like Pershing was eager to get a move on with the operation. If they gave the Institute too much time to regroup there was a very real chance that they would be forced out by the sheer numbers of Synths that the Institute would throw at them.

"Got it!" Sturges finally said, as he looked up away from the terminal and towards the leaders. "Reinforcements are on their way" Just as he finished saying that, the blue hue of the Institute teleporter flashed in the teleporter room, with both Minutemen and powered armored Brotherhood soldiers were teleported from the surface.

"Excellent" Maxson said, he looked over at the General and said "We should get a move on" Pershing nodded and began to give the order when Preston spoke up from behind him.

"Sturges, if anyone comes through here looking for a way out, let them through." He looked around and finished "we are not here to murder these people."

Pershing then said "Teleport them to a place where they can be easily contained, like the Castle, so after this we can figure out what were going to do with the survivors."

Maxson had moved to his right and said "That is acceptable to the Brotherhood, but if anyone gets in our way shoot to kill." The Brotherhood soldiers stated their agreements, while the Minutemen did not. Maxson either did not notice or did not care that the Minuteman did not agree, as he turned to Pershing and said "Lets move out"

Pershing motioned for the force of soldiers to move out and they moved single file down the stair well leading to the elevator to the Institute proper. Pershing walked into the elevator and pressed the button and nothing happened. Pershing cursed and turned around "Were going to need to find another way around, the Institute has locked down the elevator."

Danse, who still had the gas helmet on, spoke up from behind a couple of Minutemen soldiers "There is a door open over here "he opened the door and said "It's unlocked!" Pershing saw some of the Brotherhood keep an eye on Danse and one of the Knights leaned over and spoke to another soldier. Pershing knew that it was dangerous to bring Danse along, but he needed his best soldiers on this mission, so the risk was worth it.

Pershing moved through the mass of soldiers and entered into the room. This part of the Institute was a far cry from the parts that Pershing had visited, this was covered in dust and rust, while the Institute proper was much cleaner. Maxson stated what everyone was thinking, "So this is the Institute? I expected more from them."

Preston stated "This can't be how they have lived for two hundred years."

The group of soldiers made their way through the what looked to be a robotics factory. They had run into a few turrets which had been brushed aside by the small army. Pershing ordered some of his men to take a position at the windows as it overlooked what looked to be the main room of the robotics factory, several synths and a de-activated sentry had taken up position. "They're going to try to stop us there" Pershing said pointing towards the synths. He then looked at Preston and asked "You brought grenades, right?"

Preston nodded and grabbed his satchel, emptying its contents showing eight grenades. Pershing smiled and directed Garvey to hand out the grenades as the rest of the team moved down towards the main area.

Maxson had already moved on ahead with the Brotherhood soldiers at his side, including Paladin Brandis. They had purged the synth forces in the stairwells leading down to the floor of the robotics factory. Maxson and his soldiers now stood on the main floor watching as the synth abominations tried to get a old sentry bot working. Just has we was getting ready to order the attack, Pershing slid to the right of him, also looking at the synths. "I left Preston and some of the Minutemen back up there, once we open fire they're going to let loose with grenades. Maxson nodded and gave the order to attack. He and the General stood up and opened up fire with their respective weapons, Maxson's a modified Gatling Laser, and the General's a old R-91 Assault Rifle. As they opened fire, many of the synths fell, and the other synths responded with fire, they themselves were destroyed by shrapnel coming from grenades.

"Very well done" A Minuteman to the left of Maxson said, he looked over and saw that it was the Minuteman wearing the gas mask, Danse. Arthur felt his blood boil, why had Pershing brought that thing with him to destroy the Institute, it invalidated nearly everything about the agreement that they had made regarding Danse! He couldn't make a big deal about it here, as they had bigger things to worry about than one synth that was aiding them, but when he and the General were alone, he would bring it up.

As he finished up that line of thought, the army found a hole in the floor towards the back of the robotics factory that they dropped down from, with only one exit. The exit led to a far cleaner portion of the Institute, where there was no rust. The army then emerged from the room into a large circular room with the back of the room showing an enclosed habitat some sort of animal that Maxson did not recognize. They were also fired upon by Institute synths who were now desperately trying to repel the invaders, they were brushed aside and destroyed.

Just as they were preparing to push on into what Pershing said was the hub of the Institute, the windows at the habitat housing the animals slid up allowing the animals to attack the closet soldiers, two Minuteman were ripped in half and Paladin Brandis was knocked down as one of the animals attempted to claw their way into the armor. By this point however, Maxson and the rest of the army were now firing at the animals killing both of them before they could do more damage. Brandis was slow to get up, but he did. "Are you alright sir?" one of the Brotherhood scribe medics asked. Brandis simply brushed him aside and stated that he was fine.

Pershing then said "We need to get going, the Institute is probably setting up barricades as we speak." Maxson nodded and they broke their way into the next room. Institute scientists and their synths awaited them and opened fire, two more Minutemen fell, as did a Brotherhood lite Knight but they forced their way towards the central elevator. Institute coursers and their synths were also relayed into the battle, and while the slowed down the speed of the force, they did not stop it. The fighting raged on for nearly an hour, but finally the last of the synth army was either destroyed or forced to retreat.

"Sirs!" a Minuteman engineer yelled from the door leading to the advanced systems of the Institute, and continued as both Pershing and Maxson arrived "They have locked the doors, we can't get through."

Pershing once again found himself cursing himself. He should have thought about that instead now they were forced to wait and allow for the Institute to overwhelm them! But then he remembered something, Shaun was the Director of this place and he could probably override the lockdown from the terminal. "I have an idea; you should stay here and prepare yorusleves in case this works." And without waiting for an answer he walked off in the direction of Shaun's room. As he passed the elevator, it opened and allowed him access to the room, where he found Shaun lying on his bed.

He walked over to him and said "I'm sorry its come to this Shaun."

Shaun's face turned to one of disgust on it and he said" You're sorry? You must not be sorry enough if you're here actually going through with this." he coughed and then continued" Its not enough that I lay here dying, now you plan to destroy everything, under what righteous pretext have committed this atrocity?"

John kneeled down and answered "After you attacked the Minutemen, the Brotherhood? Tried to seize control of the Commonwealth? After you spent nearly a hundred years kidnapping people and replacing them with Synths? And you can't imagine why I'm standing here?"

"I did not want to have to count you among my enemies Father." He looked away from Pershing and said "But now you are here and you are going to destroy everything I have to worked to help build."

"Help me son, there doesn't have to be any more bloodshed today, help me shut down the synths and give us a easy way to the reactor." Pershing pleaded.

Shaun's head snapped back to him and stated "I will do no such thing, if you wish to destroy the Institute, you will have to do that on your own.

Pershing nodded and without saying another word, walked over to the terminal and ordered the lockdown shutdown, and also ordered for the Institute to be evacuated. Hoping that those who could would now be able to get out, he got up and took one final look at Shaun, and walked out of the room. The sounds of battle alerted him that the Synths were once again attacking the army in the hub section. He rushed down, killing several synths as they attacked him, and saw what was attacking them. Synths armed with rocket launchers had pinned the Minutemen down but the Brotherhood was slowly pushing them back.

Pershing regrouped with them and they pressed on. They entered into the Advanced Systems Section and once again were stopped in the tight corridors by Institute scientists and their synths, but they were slowly pushed back as they broke into another long hallway. The hallway was back to being rusty and run down, similar to the old robotics area where they had entered.

They slowly fought through the area and destroyed the synths along the way, until they found themselves looking at the reactor, which was housed inside of a protective shield. What remained of the Synths and the few Institute scientists not willing to leave were all that was left? Both the Minuteman and Brotherhood soldiers dispatched them.

"Now all we need to attach the charge to the generator" Maxson said. Both he and Pershing walked up to the door leading to the reactor.

"Let me do it." Pershing said and he opened up the door and walked into the room and attached the pulse charge onto the generator. 

"Ingram teleport us out of here!" Maxson yelled, and then they were all teleported, not however out of the Institute but back at the teleporter room. "Ingram what are we doing here?"

"We were going to relay you out sir, but this child showed up claiming to be the General's on." Ingram answered gesturing towards the child.

Pershing walked up to the child, and kneeled down, he appeared to be about ten years old and the child looked at him. "Please Dad take me with you!"

Pershing did not know how to feel about this, but he knew couldn't let this scared child stay here. "Ok son, let go" he looked up to Sturges and said "Make sure that he gets out and back to the Castle safely."

"Will do General"

Pershing then stood up and walked back to the relay and then he found himself on top of the Mass Fusion building overlooking the area where the Commonwealth Institute of Technology used to be located.

"That button is hooked up to the fusion pulse charge, one push and the "best hope for humanity" will go up in smoke." Preston said.

Pershing walked up to the button and flipped the switches to the on position and opened up the button cover. He hesitated and then pressed the button and a new age for the Commonwealth began.


	7. Epilogue

**A/N: I do not own Fallout 4 or the characters mentioned in this story.**

General John Pershing had just closed his eyes when he felt the Vertibird begin its descent as the vertibird made its approach to Diamond City. He kept his eyes closed for a few more seconds before opening them and looked at his collegues in the vertibird with him.

Preston Garvey, Pershing's second-in-command, sat to his right with a determined look on his face as he focused on not throwing up. Preston wasn't nearly as used to flying on a vertibird as the other people on the air craft. In front of Pershing sat Elder Arthur Maxson who despite the now noticeable bags underneath his eyes remained alert and focused on the mission ahead.

The mission ahead being that the two powers needed to announce their victory over the Institute. After a quick discussion between Pershing and Maxson it was agreed that Diamond City would be the most appropriate place for the announcement, as it was home to the main radio station, and it was the sight of the first Gen 3 synth to operate in the Commonwealth.

The vertibird landed just outside of the entrance to Diamond City and the group got out of the vertibird. Pershing and Maxson both stood at the head of the group of Minutemen and Brotherhood soldiers as they began to head into the city when they were stopped by the appearance of Diamond City's mayor, Mcdonough.

"Gentlemen" he said as he walked up to Pershing and Maxson "As the elected representative of our fine city I welcome you." He held put his hand and both Maxson and Pershing shook it. His happy appearance then turned to annoyance as he asked "Why is both the General of the Minutemen and the Elder of the Brotherhood doing here at my city?"

Pershing didn't like how Mcdonough had called Diamond City his city, but that was not important right now. "Mayor Mcdonough, I am sure you noticed the large explosion to the north nearly an hour ago?" Mcdonough shook his head and Pershing continued "After a joint operation the Minutemen and the Brotherhood have destroyed the Institute.

Mcdonough's eyes looked like they would pop out of their sockets as he heard that. "Are you saying…." He trailed off.

Maxson answered him "Yes the Institute has been laid low by our combined forces, and we would like to use the radio station to announce that fact to the rest of the Commonwealth."

Mcdonough's shocked expression did not leave him, but he allowed the group to enter the city. Much of the populace which had been going about it's day stopped what they were doing to look at the group of Minutemen and Brotherhood soldiers as they moved their way through the crowded market. Pershing caught sight of the synth detective Nick Valentine who simply smiled and nodded his head in congratulations. Pershing nodded his head as well as he passed.

Someone must have run ahead to tell Travis of who was coming, because when they got to the trailer that housed Diamond City Radio, Travis Miles was out front. "It's all ready for you're speech"

Pershing smiled and thanked him quickly as both he and Maxson entered the trailer. They both took a seat in front of the same microphone, and after making sure that it was on, Pershing began. "People of the Commonwealth, this is General John Pershing of the Commonwealth Minutemen"

Maxson then cut in "And Elder Arthur Maxson of the Brotherhood of Steel"

Both Pershing and Maxson looked at each other and with a nonverbal agreement Pershing continued "I have no doubt that many of you saw the explosion in Cambridge some time ago and wondered what that was." Pershing paused for a second before continuing on "That was the Commonwealth's boogieman, the Institute."

Maxson then began "After years of you being afraid of the Institute and it's synths you are now free to live your lives in peace. "He paused gathering a breath and then continued "This is a victory that was achieved only by the hard-won sacrifices of Brotherhood and Minutemen soldiers"

Pershing then spoke "With the destruction of the Institute, the Commonwealth has been freed from the paranoia it caused, and we wish to see the Commonwealth stabilize. Please know that the Minutemen stand ready at a minute's notice to protect the people."

Not to be out done Maxson added on "And the Brotherhood will now be able to begin prosecuting operations against the Super Mutants in downtown Boston."

"But for now, please take pleasure in the fact that the Minutemen and the Brotherhood have achieved victory over the Institute. This concludes the broadcast." Pershing and Maxson laid back in their chairs.

Maxson looked over at him and said "I am going back to the Prydwen to address my soldiers, are you to remain here or do you want to go back to the Castle?"

"I need to get back to the Castle" Maxson nodded and then stood, thanked Travis and left, followed by Pershing. They quickly bordered the vertibird outside of the city and were then on their way to the Castle. The ride to the Castle was silent everyone either too tired to speak, or had to much on their minds. After a while the aircraft landed and the Minutemen portion of the group quickly dismounted and saw the vertibird off.

Garvey and Danse stood next to Pershing as they watched the vertibird leave. "Well that's done" Garvey said, he looked to the General "Now we just need to figure out about the future."

Pershing smiled but said "That can be done tomorrow, for now let's celebrate the fact that their will be a future for us to figure out"

"I can do that" Garvey agreed, and then the three soldiers went into the Castle, where celebrations were being held.

* * *

_Despite their combined victory over the Institute, tensions soon rose between the Commonwealth Minutemen and the Brotherhood of Steel over how best to organize the post Institute Commonwealth. _

_Diamond City stood at the center of this conflict, as shortly after the Destruction of the Institute, Mayor Mcdonough was proven to be a synth spy and was summarily executed. Diamond City in the days after this event looked to be sliding into anarchy and confusion before the Commonwealth Minutemen occupied the city three weeks after the Destruction of the Institute. _

_Between this and other conflicts to many it looked as though the Destruction of the Institute would not bring peace to a Commonwealth that desperately needed it, instead it looked as though the Minutemen and the Brotherhood would slide into war. _

**A/N: It's hard to believe that I began writing this story back in December. I must say that I am quite disappointed in myself for letting myself take this long to finish it. But this story is now finished and I wanted to thank everyone for taking the time to this read this story. **


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